ArticleRNA (New York, N.Y.)2002
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.
Article in RNA (New York, N.Y.), 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 197 papers.
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Who cites it
197 citing papers in PubMed, 371 citations in OpenAlex.
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- Archaeal RNA processing and regulation: expanding the functional landscape.Microbiology and molecular biology reviews : MMBR · 2025Review
- tsRNA in head and neck tumors: Opportunities and challenges in the field.Non-coding RNA research · 2025Review
- Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display.Nucleic acids research · 2025Article
- Analyzing, visualizing, and annotating tRNA-derived RNAs using tRAX and tDRnamer.Methods in enzymology · 2025Article
- Genomic factors shaping codon usage across the Saccharomycotina subphylum.G3 (Bethesda, Md.) · 2024Article
- Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.Nucleic acids research · 2024Article
- The life and times of a tRNA.RNA (New York, N.Y.) · 2023Review
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- On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes.RNA biology · 2023Article
- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Intron-Dependent or Independent Pseudouridylation of Precursor tRNA Containing Atypical Introns inInternational journal of molecular sciences · 2022Article
- Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures.Nucleic acids research · 2022Article
- Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The C nucleotide at the mature 5' end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3' terminus as well as functionality.Nucleic acids research · 2022Article
- Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.Molecular biology and evolution · 2022Article
- Overview of tRNA Modifications in Chloroplasts.Microorganisms · 2022Article
- Unconventional genetic code systems in archaea.Frontiers in microbiology · 2022Review
137 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.